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Some time before the Battle of Endor, Leia Organa is running through a Rebelcruiser with Luke Skywalker at her heels. Leia is about to depart on a mission to the planetYinchorr, and Skywalker tries to convince her to let him go with her. However, in an attempt to earn the Yinchorri's trust, she has agreed to not bring any Rebel soldiers with her. Skywalker is still worried for her, since there is Imperial activity in that sector, and he gives her an emergency beacon to signal him in case she runs into trouble. A Yinchorri shuttle arrives to take Leia to the desert world, but on the way there, the Yinchorri commander reveals that she is actually going to be used as a hostage to trade to the Empire for the safety of the Yinchorri Elder Council, whom Imperial GovernorMarcellin Wessel has captured. However, on the way to turn over the Princess, their TIE fighter escort begins to fire on them, as Wessel is content to just kill the Rebel leader. As the Yinchorri panic, Leia springs into action, takes control of the blaster cannon, and fires back. The Yinchorri pilot is able to outfly the TIEs, and Leia shoots down one of the starfighters. However, right as Leia shoots down the second starfighter, their ship is hit by the Imperial craft's weapons, and both ships crash land in the desert below. Immediately before the crash, Leia is able to activate her emergency beacon. Back with the Alliance Fleet, Luke, Chewbacca, and Lando Calrissian receive the signal and leave immediately in the Millennium Falcon to rescue her. Back on Yinchorr, a stormtrooper reports to Wessel, telling him that Princess Leia's ship was shot down but that both TIE fighters were destroyed as well. Wessel, wanting to confirm Leia's death, organizes a party to track down the crashed shuttle.

At the same time, the TIE pilot of the second craft has survived, and he makes his way to the crashed Yinchorri shuttle. Although the man has orders to kill the passengers of the Yinchorri shuttle, he recognizes Leia and decides to ignore orders, freeing her. The TIE pilot is actually from Alderaan, and before joining the Empire, he had been a common servant on the world. Leia, shocked that an Alderaanian would serve the Empire, calls the man a traitor to his homeworld. Despite her insults, the Imperial helps her to safety, claiming that Leia's father, and not the Empire, was to blame for opposing the Empire and causing Alderaan's destruction. As the two argue, they are oblivious to the fact that they are being stalked by the rolk-mahgir, fearsome native beasts. In their continuing trek across the desert, Leia attempts to make her captor realize the evils of the Empire. He shows her a small rock from Alderaan, bought from a trader on Tatooine. The Imperial has fashioned the rock into a necklace, as his own souvenir of his lost homeworld. Leia is outraged by his attitude towards the destruction of Alderaan, claiming that the memento is a symbol of the slaughter of millions. Drawn to their loud outbursts, the rolk-mangir attack, grabbing the Imperial by his leg.

Leia is able to get ahold of the man's blaster, and she fires on the beasts, driving them away and saving the Imperial's life. Meanwhile, Luke, Lando, and Chewbacca have arrived above Yinchorr tracking Leia's emergency signal. However, Wessel's group is also closing in on Leia's signal, and they are about to arrive at her position. Trying to escape the rolk-mahgir, Leia and the Imperial are forced to dive off a cliff to a lower ledge to avoid the beasts. In the jump, Leia nearly slips off the ledge to her death, but the Imperial grabs her arm and pulls her to safety. The two begin to reminisce about Alderaan, but Leia once again brings up the destruction of Alderaan, still appalled over the man's service to the Empire. Sensing that there is still some good in the soldier, she asks him to come with her and join the Rebellion. The Imperial is still hesitant to leave the Empire, claiming that it is too much of a risk to give up all he has for "a dream that might never come true".

When Leia claims that he is not even a man if he believes that, he is greatly offended and points his blaster at her, deciding to take her to the approaching Imperials. Wessel is pleased with finding the princess, and he immediately orders his men to kill the Yinchorri council, claiming that Leia is next. The Imperial soldier is shocked at Wessel's cruelty, beginning to see the truth in Leia's words. Before Wessel can execute Leia, the Millennium Falcon comes to the rescue and destroys Wessel's ground vehicle. In the resulting chaos, Leia runs for the ship, but Wessel attempts one last time to kill the princess, aiming his gun at the woman. The Imperial recognizes Wessel's intent, and he shoots Wessel's gun out of his hand. He claims that Leia was right about the Empire, and the two make their way to the Millennium Falcon which has landed a short distance away. However, before they can board the ship, the Imperial soldier is shot by one of Wessel's men. Leia grabs the man's hand as the ship lifts off, pulling him into the air. The Imperial struggles to hold onto her hand, but he is too weak from his injuries and slips from her fingers, falling to his death. As Lando and Luke pull her into the ship, Leia looks into her hand where she is still holding the Imperial's Alderaanian rock and begins to cry.

The spelling of "Yinchor" was changed in later mentions, adding a second "r" to the name. In the same fashion, the "Rolk-mahgir" had their name changed to the "Rolk-mangir" in later mentions.

This issue was the only Marvel Star Wars issue written by Randy Stradley, who later went on to work for Dark Horse Comics. After this comic, Stradley was asked to write another story by editor Ann Nocenti, but she wanted the story to involve Hoojibs. Stradley found it difficult to write an exciting story about "telepathic bunnies," and so "The Alderaan Factor" was the first and last job that he did for Marvel.[2] After the Star Wars comics license went to Dark Horse, Stradley would write two other comics stories under their publication involving the planet Yinchorr: Jedi Council: Acts of War and Crimson Empire.